Please use mvd regarding this concern ....it will obiously give u good results with graphical representationj

Fep

I am suggesting to use glide of schrodinger suit.

Hi ManojKumar, i can suggest u to use Auto-dock software it is free of cost, and if u have glide module in Schrodinger suit that will be on of the best docking software for docking analysis. If u know the active site of the target protein then ur docking will be simple but if u don't have the information about active site..it will separate story. The binding affinity of the compound can be determine using free energy binding and docking score this information u can get from auto dock as well as in glide software. First study the interacting mode of ur ligand with ur target protein then modify the ligand accordance to that of free energy and do docking with newly drawn compound. Before that u read about the docking and its analysis. I support the Brian D Marsden said. For exact binding affinity of ur ligand with ur targhet protein can be determined in experimentally using ITC or crystallography.

Hi Manojkumar, what help do you exactly need? Being specific can fetch you a lot more valuble suggestions.

Thanks a lot guys for your replies. Actually i am not much aware of the bioinformatic sofwares so i will be very thankfull to you if you tell me what are the step to be performed in the respective softwares. guys i Know the target site where the drug molecule will go on bind to the protein. once i build a molecule which have more binding affinity to the protein than the traditional drug i am going for the crystallography to see the exact interaction. so guys please help me. thanking you.

HI manoj, If u use the free software (Autodock) then u can follow the link given below for installation of the software and tutorial for doing docking.

1. http://www.youtube.com/watch?v=LQHvlH0Hq0I&feature=related

2. http://www.youtube.com/watch?v=awGrWBEk8Q0&feature=related

3. http://www.youtube.com/watch?v=H_ChiGTpZd4&feature=related

4. http://www.youtube.com/watch?v=KScj5jpAlno&feature=related

5. http://www.youtube.com/watch?v=zZdr2LwPIqg&feature=related

hi manoj, if u plan to use free software u can use autodock. Installation of the software and running program u can follow the link.

http://www.youtube.com/watch?v=LQHvlH0Hq0I&feature=related

U can use tutorial for that

Thanks, I am also interested in docking my protein with different isomers of a compound (ligand).How do I interprete my result so that I can mutate at particular C-position? to ensure & improve high catalytic property of my protein.

hi Ajao, If u are using isomers for docking analysis and u want to interpret the results u should have chemistry knowledge or u can get literature information. Some people already down so many docking work using isomers if u refer that it will be useful for u to interpret ur docking results.

Thanks Kannan, I 'll get back to you!

hi Ajao,

here i have attached tutorial which we used for previous workshop conducted in pondicherry university, it might help u............. this tutorial is based on autodock software.......

hi Manoj, AUTODOCK is good for docking small molecules to the ligand/sbstrate binding site.Docking programs not always give u the correct quantitative information about binding, but it may give u a probable binding mode.

Kanan,

I am so much grateful, is very helpful.Thanks